Class MemoryBasedReadEndsForMarkDuplicatesMap

    • Constructor Detail

      • MemoryBasedReadEndsForMarkDuplicatesMap

        public MemoryBasedReadEndsForMarkDuplicatesMap()
    • Method Detail

      • remove

        public ReadEndsForMarkDuplicates remove​(int mateSequenceIndex,
                                                String key)
        Description copied from interface: ReadEndsForMarkDuplicatesMap
        Remove element with given key from the map. Because an implementation may be disk-based, the object returned may not be the same object that was put into the map
        Specified by:
        remove in interface ReadEndsForMarkDuplicatesMap
        Parameters:
        mateSequenceIndex - must agree with the value used when the object was put into the map
        key - typically, concatenation of read group ID and read name
        Returns:
        null if the key is not found, otherwise the object removed.
      • put

        public void put​(int mateSequenceIndex,
                        String key,
                        ReadEndsForMarkDuplicates readEnds)
        Description copied from interface: ReadEndsForMarkDuplicatesMap
        Store the element in the map with the given key. It is assumed that the element is not already present in the map.
        Specified by:
        put in interface ReadEndsForMarkDuplicatesMap
        Parameters:
        mateSequenceIndex - use to optimize storage & retrieval. The same value must be used when trying to remove this element. It is not valid to store the same key with two different mateSequenceIndexes.
        key - typically, concatenation of read group ID and read name
        readEnds - the object to be stored